Starting phenix.real_space_refine on Wed Mar 4 02:14:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nts_0510/03_2026/6nts_0510.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nts_0510/03_2026/6nts_0510.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6nts_0510/03_2026/6nts_0510.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nts_0510/03_2026/6nts_0510.map" model { file = "/net/cci-nas-00/data/ceres_data/6nts_0510/03_2026/6nts_0510.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nts_0510/03_2026/6nts_0510.cif" } resolution = 3.63 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mn 2 7.51 5 S 57 5.16 5 C 6378 2.51 5 N 1654 2.21 5 O 1862 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9956 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4543 Classifications: {'peptide': 583} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 556} Chain: "B" Number of atoms: 2976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2976 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 17, 'TRANS': 343} Chain: "C" Number of atoms: 2399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2399 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 11, 'TRANS': 284} Chain breaks: 1 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'L2J': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.99, per 1000 atoms: 0.20 Number of scatterers: 9956 At special positions: 0 Unit cell: (96.824, 110.656, 118.104, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 2 24.99 S 57 16.00 F 3 9.00 O 1862 8.00 N 1654 7.00 C 6378 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 556.6 milliseconds 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2378 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 3 sheets defined 74.9% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 11 through 17 Processing helix chain 'A' and resid 24 through 43 removed outlier: 3.506A pdb=" N ARG A 28 " --> pdb=" O ASP A 24 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N SER A 36 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N THR A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA A 41 " --> pdb=" O THR A 37 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY A 43 " --> pdb=" O ALA A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 59 removed outlier: 5.099A pdb=" N LEU A 52 " --> pdb=" O ARG A 48 " (cutoff:3.500A) Proline residue: A 53 - end of helix Processing helix chain 'A' and resid 62 through 76 Processing helix chain 'A' and resid 84 through 88 removed outlier: 4.149A pdb=" N HIS A 87 " --> pdb=" O GLU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 98 removed outlier: 3.867A pdb=" N LEU A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 116 removed outlier: 3.736A pdb=" N ARG A 105 " --> pdb=" O GLU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 137 removed outlier: 4.837A pdb=" N VAL A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) Proline residue: A 130 - end of helix Processing helix chain 'A' and resid 140 through 148 removed outlier: 3.804A pdb=" N ARG A 144 " --> pdb=" O TRP A 140 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS A 148 " --> pdb=" O ARG A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 155 Processing helix chain 'A' and resid 162 through 175 removed outlier: 3.692A pdb=" N GLN A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 193 removed outlier: 3.529A pdb=" N ARG A 182 " --> pdb=" O THR A 178 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N GLY A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N GLU A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 214 removed outlier: 5.081A pdb=" N ILE A 206 " --> pdb=" O LYS A 202 " (cutoff:3.500A) Proline residue: A 207 - end of helix Processing helix chain 'A' and resid 217 through 233 removed outlier: 4.698A pdb=" N VAL A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ASN A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 244 removed outlier: 4.398A pdb=" N GLU A 241 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ALA A 242 " --> pdb=" O GLU A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 253 removed outlier: 3.666A pdb=" N GLU A 253 " --> pdb=" O ARG A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 266 Processing helix chain 'A' and resid 266 through 275 removed outlier: 3.907A pdb=" N ALA A 273 " --> pdb=" O GLU A 269 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY A 275 " --> pdb=" O GLN A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 292 removed outlier: 4.743A pdb=" N VAL A 284 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Proline residue: A 285 - end of helix removed outlier: 3.567A pdb=" N LYS A 292 " --> pdb=" O GLN A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 312 removed outlier: 4.821A pdb=" N LYS A 307 " --> pdb=" O SER A 303 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N GLU A 308 " --> pdb=" O HIS A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 326 removed outlier: 3.565A pdb=" N VAL A 321 " --> pdb=" O CYS A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 335 removed outlier: 3.767A pdb=" N LYS A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N GLU A 332 " --> pdb=" O PRO A 328 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU A 333 " --> pdb=" O CYS A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 350 removed outlier: 3.935A pdb=" N LYS A 342 " --> pdb=" O ASN A 338 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER A 347 " --> pdb=" O SER A 343 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL A 348 " --> pdb=" O ALA A 344 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N MET A 350 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 357 through 374 removed outlier: 3.806A pdb=" N ILE A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLU A 363 " --> pdb=" O ASP A 359 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU A 366 " --> pdb=" O ILE A 362 " (cutoff:3.500A) Proline residue: A 367 - end of helix Processing helix chain 'A' and resid 377 through 387 removed outlier: 3.680A pdb=" N ASN A 387 " --> pdb=" O ASN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 391 removed outlier: 3.816A pdb=" N VAL A 391 " --> pdb=" O LEU A 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 388 through 391' Processing helix chain 'A' and resid 396 through 412 removed outlier: 3.760A pdb=" N SER A 403 " --> pdb=" O GLN A 399 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU A 405 " --> pdb=" O SER A 401 " (cutoff:3.500A) Proline residue: A 406 - end of helix Processing helix chain 'A' and resid 416 through 435 removed outlier: 3.626A pdb=" N ARG A 420 " --> pdb=" O LYS A 416 " (cutoff:3.500A) Proline residue: A 428 - end of helix Processing helix chain 'A' and resid 435 through 443 removed outlier: 3.956A pdb=" N PHE A 439 " --> pdb=" O GLY A 435 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP A 440 " --> pdb=" O VAL A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 452 removed outlier: 3.599A pdb=" N CYS A 447 " --> pdb=" O LEU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 474 removed outlier: 3.556A pdb=" N ARG A 459 " --> pdb=" O VAL A 455 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU A 471 " --> pdb=" O LYS A 467 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS A 472 " --> pdb=" O LYS A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 481 removed outlier: 3.957A pdb=" N ALA A 478 " --> pdb=" O GLY A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 489 removed outlier: 3.799A pdb=" N LYS A 485 " --> pdb=" O THR A 481 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N MET A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 494 through 513 removed outlier: 3.734A pdb=" N THR A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR A 501 " --> pdb=" O HIS A 497 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASN A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL A 511 " --> pdb=" O VAL A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 529 removed outlier: 3.611A pdb=" N THR A 517 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N LEU A 522 " --> pdb=" O THR A 518 " (cutoff:3.500A) Proline residue: A 523 - end of helix removed outlier: 3.575A pdb=" N ALA A 529 " --> pdb=" O VAL A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 548 removed outlier: 4.549A pdb=" N ALA A 541 " --> pdb=" O ARG A 537 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS A 546 " --> pdb=" O LYS A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 551 No H-bonds generated for 'chain 'A' and resid 549 through 551' Processing helix chain 'A' and resid 552 through 569 removed outlier: 3.538A pdb=" N LEU A 556 " --> pdb=" O ASP A 552 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN A 557 " --> pdb=" O ASN A 553 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LYS A 561 " --> pdb=" O GLN A 557 " (cutoff:3.500A) Proline residue: A 562 - end of helix removed outlier: 3.814A pdb=" N GLN A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 587 Processing helix chain 'B' and resid 69 through 76 removed outlier: 4.037A pdb=" N GLN B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LYS B 74 " --> pdb=" O LEU B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 81 Processing helix chain 'B' and resid 91 through 111 removed outlier: 3.930A pdb=" N GLU B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU B 106 " --> pdb=" O ASN B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 132 removed outlier: 3.668A pdb=" N TYR B 120 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N SER B 121 " --> pdb=" O GLU B 117 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASP B 122 " --> pdb=" O SER B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 171 removed outlier: 4.230A pdb=" N LEU B 161 " --> pdb=" O PRO B 157 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL B 162 " --> pdb=" O HIS B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 181 Processing helix chain 'B' and resid 185 through 194 Processing helix chain 'B' and resid 195 through 198 Processing helix chain 'B' and resid 200 through 218 removed outlier: 3.565A pdb=" N ARG B 204 " --> pdb=" O ASP B 200 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 238 Processing helix chain 'B' and resid 245 through 257 removed outlier: 3.552A pdb=" N LEU B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE B 252 " --> pdb=" O GLU B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 260 No H-bonds generated for 'chain 'B' and resid 258 through 260' Processing helix chain 'B' and resid 265 through 275 removed outlier: 3.713A pdb=" N LEU B 272 " --> pdb=" O HIS B 268 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N MET B 273 " --> pdb=" O LYS B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 282 removed outlier: 3.698A pdb=" N THR B 281 " --> pdb=" O PRO B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 287 Processing helix chain 'B' and resid 288 through 301 removed outlier: 3.856A pdb=" N PHE B 299 " --> pdb=" O CYS B 295 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU B 300 " --> pdb=" O VAL B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 305 No H-bonds generated for 'chain 'B' and resid 303 through 305' Processing helix chain 'B' and resid 306 through 317 removed outlier: 3.698A pdb=" N VAL B 310 " --> pdb=" O LEU B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 337 removed outlier: 3.600A pdb=" N MET B 328 " --> pdb=" O GLN B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 362 removed outlier: 4.465A pdb=" N LYS B 347 " --> pdb=" O THR B 343 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ILE B 348 " --> pdb=" O GLN B 344 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLU B 350 " --> pdb=" O LYS B 346 " (cutoff:3.500A) Proline residue: B 351 - end of helix removed outlier: 3.623A pdb=" N LYS B 358 " --> pdb=" O LYS B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 373 Processing helix chain 'B' and resid 374 through 376 No H-bonds generated for 'chain 'B' and resid 374 through 376' Processing helix chain 'B' and resid 377 through 386 Processing helix chain 'B' and resid 391 through 402 removed outlier: 4.139A pdb=" N PHE B 396 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA B 397 " --> pdb=" O PRO B 393 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 425 removed outlier: 3.540A pdb=" N VAL B 412 " --> pdb=" O ASN B 408 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N MET B 425 " --> pdb=" O THR B 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 19 Processing helix chain 'C' and resid 24 through 40 Processing helix chain 'C' and resid 61 through 73 Processing helix chain 'C' and resid 92 through 107 Processing helix chain 'C' and resid 120 through 127 Processing helix chain 'C' and resid 128 through 138 Processing helix chain 'C' and resid 140 through 151 removed outlier: 3.548A pdb=" N ASP C 151 " --> pdb=" O THR C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 183 removed outlier: 3.601A pdb=" N ILE C 180 " --> pdb=" O THR C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 201 Processing helix chain 'C' and resid 221 through 233 Processing helix chain 'C' and resid 264 through 268 Processing sheet with id=AA1, first strand: chain 'C' and resid 45 through 48 removed outlier: 6.154A pdb=" N GLN C 46 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N PHE C 164 " --> pdb=" O SER C 238 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL C 237 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ILE C 259 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ARG C 239 " --> pdb=" O ILE C 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 111 through 113 removed outlier: 6.108A pdb=" N THR C 53 " --> pdb=" O LEU C 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 202 through 203 removed outlier: 3.503A pdb=" N PHE C 220 " --> pdb=" O ASP C 202 " (cutoff:3.500A) 528 hydrogen bonds defined for protein. 1536 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.53 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.57: 10076 1.57 - 1.92: 84 1.92 - 2.27: 0 2.27 - 2.62: 0 2.62 - 2.97: 1 Bond restraints: 10161 Sorted by residual: bond pdb=" C10 MLL C 309 " pdb=" O9 MLL C 309 " ideal model delta sigma weight residual 1.427 2.965 -1.538 2.00e-02 2.50e+03 5.92e+03 bond pdb=" C02 L2J A 601 " pdb=" C03 L2J A 601 " ideal model delta sigma weight residual 1.396 1.293 0.103 2.00e-02 2.50e+03 2.64e+01 bond pdb=" C01 L2J A 601 " pdb=" C06 L2J A 601 " ideal model delta sigma weight residual 1.388 1.488 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" C MLL C 309 " pdb=" O9 MLL C 309 " ideal model delta sigma weight residual 1.327 1.231 0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" C07 L2J A 601 " pdb=" C08 L2J A 601 " ideal model delta sigma weight residual 1.402 1.320 0.082 2.00e-02 2.50e+03 1.70e+01 ... (remaining 10156 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.18: 13721 3.18 - 6.35: 53 6.35 - 9.53: 1 9.53 - 12.70: 3 12.70 - 15.88: 2 Bond angle restraints: 13780 Sorted by residual: angle pdb=" O03 L2J A 601 " pdb=" S01 L2J A 601 " pdb=" O04 L2J A 601 " ideal model delta sigma weight residual 116.82 100.94 15.88 3.00e+00 1.11e-01 2.80e+01 angle pdb=" C MLL C 309 " pdb=" O9 MLL C 309 " pdb=" C10 MLL C 309 " ideal model delta sigma weight residual 117.67 133.31 -15.64 3.00e+00 1.11e-01 2.72e+01 angle pdb=" C19 L2J A 601 " pdb=" S01 L2J A 601 " pdb=" N02 L2J A 601 " ideal model delta sigma weight residual 100.55 111.98 -11.43 3.00e+00 1.11e-01 1.45e+01 angle pdb=" C01 L2J A 601 " pdb=" C06 L2J A 601 " pdb=" C05 L2J A 601 " ideal model delta sigma weight residual 119.28 108.25 11.03 3.00e+00 1.11e-01 1.35e+01 angle pdb=" CA MLL C 309 " pdb=" C MLL C 309 " pdb=" O9 MLL C 309 " ideal model delta sigma weight residual 110.79 121.00 -10.21 3.00e+00 1.11e-01 1.16e+01 ... (remaining 13775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 5703 17.83 - 35.65: 387 35.65 - 53.48: 69 53.48 - 71.31: 16 71.31 - 89.14: 12 Dihedral angle restraints: 6187 sinusoidal: 2536 harmonic: 3651 Sorted by residual: dihedral pdb=" CA ARG A 537 " pdb=" C ARG A 537 " pdb=" N PHE A 538 " pdb=" CA PHE A 538 " ideal model delta harmonic sigma weight residual 180.00 158.37 21.63 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA HIS B 364 " pdb=" C HIS B 364 " pdb=" N PHE B 365 " pdb=" CA PHE B 365 " ideal model delta harmonic sigma weight residual -180.00 -162.42 -17.58 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CB GLU C 188 " pdb=" CG GLU C 188 " pdb=" CD GLU C 188 " pdb=" OE1 GLU C 188 " ideal model delta sinusoidal sigma weight residual 0.00 -89.14 89.14 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 6184 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1080 0.027 - 0.055: 309 0.055 - 0.082: 116 0.082 - 0.110: 54 0.110 - 0.137: 13 Chirality restraints: 1572 Sorted by residual: chirality pdb=" C18 L2J A 601 " pdb=" C13 L2J A 601 " pdb=" C17 L2J A 601 " pdb=" N01 L2J A 601 " both_signs ideal model delta sigma weight residual False -2.31 -2.45 0.14 2.00e-01 2.50e+01 4.72e-01 chirality pdb=" CA VAL C 52 " pdb=" N VAL C 52 " pdb=" C VAL C 52 " pdb=" CB VAL C 52 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.56e-01 chirality pdb=" CA PHE A 538 " pdb=" N PHE A 538 " pdb=" C PHE A 538 " pdb=" CB PHE A 538 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.13 2.00e-01 2.50e+01 3.91e-01 ... (remaining 1569 not shown) Planarity restraints: 1764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 90 " 0.015 5.00e-02 4.00e+02 2.25e-02 8.12e-01 pdb=" N PRO A 91 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO A 91 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 91 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 86 " 0.010 2.00e-02 2.50e+03 6.28e-03 7.89e-01 pdb=" CG TYR C 86 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR C 86 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR C 86 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 86 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR C 86 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 86 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR C 86 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS C 50 " -0.013 5.00e-02 4.00e+02 2.02e-02 6.53e-01 pdb=" N PRO C 51 " 0.035 5.00e-02 4.00e+02 pdb=" CA PRO C 51 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO C 51 " -0.011 5.00e-02 4.00e+02 ... (remaining 1761 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 39 2.51 - 3.11: 7867 3.11 - 3.71: 15828 3.71 - 4.30: 21974 4.30 - 4.90: 35746 Nonbonded interactions: 81454 Sorted by model distance: nonbonded pdb=" ND1 HIS C 241 " pdb="MN MN C 401 " model vdw 1.917 2.400 nonbonded pdb=" O GLY A 275 " pdb=" OG1 THR A 279 " model vdw 2.209 3.040 nonbonded pdb=" OD2 ASP C 85 " pdb="MN MN C 402 " model vdw 2.222 2.320 nonbonded pdb=" NE2 HIS C 59 " pdb="MN MN C 402 " model vdw 2.235 2.400 nonbonded pdb=" O GLY A 513 " pdb=" OG1 THR A 517 " model vdw 2.264 3.040 ... (remaining 81449 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.64 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.710 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 1.538 10161 Z= 0.780 Angle : 0.516 15.879 13780 Z= 0.247 Chirality : 0.034 0.137 1572 Planarity : 0.002 0.023 1764 Dihedral : 13.181 89.136 3809 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.22), residues: 1231 helix: -1.17 (0.17), residues: 793 sheet: -1.94 (0.87), residues: 35 loop : -1.41 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 185 TYR 0.013 0.001 TYR C 86 PHE 0.008 0.001 PHE A 538 TRP 0.010 0.000 TRP A 257 HIS 0.003 0.000 HIS B 364 Details of bonding type rmsd covalent geometry : bond 0.01559 (10161) covalent geometry : angle 0.51645 (13780) hydrogen bonds : bond 0.12700 ( 528) hydrogen bonds : angle 5.16110 ( 1536) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 GLU cc_start: 0.8284 (pp20) cc_final: 0.8055 (pp20) REVERT: B 78 CYS cc_start: 0.8890 (m) cc_final: 0.8655 (m) REVERT: B 110 THR cc_start: 0.8511 (p) cc_final: 0.8239 (p) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.1147 time to fit residues: 19.1471 Evaluate side-chains 49 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 0.2980 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.6980 chunk 117 optimal weight: 7.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 GLN A 288 GLN B 111 ASN ** B 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.051996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.044559 restraints weight = 65363.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.045724 restraints weight = 36078.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.046559 restraints weight = 23711.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.047134 restraints weight = 17414.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.047485 restraints weight = 13832.785| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3315 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3315 r_free = 0.3315 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3314 r_free = 0.3314 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3314 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 10161 Z= 0.225 Angle : 0.739 11.261 13780 Z= 0.366 Chirality : 0.045 0.182 1572 Planarity : 0.005 0.073 1764 Dihedral : 4.575 23.399 1366 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.45 % Allowed : 7.15 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.24), residues: 1231 helix: -0.28 (0.18), residues: 821 sheet: -0.66 (1.00), residues: 31 loop : -0.70 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 168 TYR 0.017 0.002 TYR B 107 PHE 0.034 0.002 PHE A 538 TRP 0.032 0.002 TRP A 477 HIS 0.019 0.002 HIS C 241 Details of bonding type rmsd covalent geometry : bond 0.00473 (10161) covalent geometry : angle 0.73858 (13780) hydrogen bonds : bond 0.03882 ( 528) hydrogen bonds : angle 4.33136 ( 1536) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 TYR cc_start: 0.6704 (OUTLIER) cc_final: 0.6483 (m-80) REVERT: B 81 LEU cc_start: 0.7769 (tp) cc_final: 0.7483 (mt) REVERT: B 112 ARG cc_start: 0.6775 (tpt170) cc_final: 0.5760 (tpt-90) outliers start: 16 outliers final: 7 residues processed: 65 average time/residue: 0.1053 time to fit residues: 9.8411 Evaluate side-chains 49 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 60 TYR Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 165 CYS Chi-restraints excluded: chain C residue 230 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 5 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 91 optimal weight: 0.0570 chunk 32 optimal weight: 0.4980 chunk 61 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 60 optimal weight: 10.0000 chunk 96 optimal weight: 5.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 GLN A 444 ASN C 249 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.052285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.044738 restraints weight = 64691.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.045905 restraints weight = 35951.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.046759 restraints weight = 23688.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.047354 restraints weight = 17388.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.047758 restraints weight = 13803.045| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3323 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3323 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10161 Z= 0.110 Angle : 0.559 8.177 13780 Z= 0.275 Chirality : 0.040 0.247 1572 Planarity : 0.003 0.035 1764 Dihedral : 4.306 21.812 1366 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.27 % Allowed : 7.78 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.25), residues: 1231 helix: 0.26 (0.19), residues: 812 sheet: -0.33 (1.06), residues: 31 loop : -0.42 (0.34), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 46 TYR 0.010 0.001 TYR B 400 PHE 0.027 0.001 PHE A 538 TRP 0.023 0.001 TRP B 156 HIS 0.003 0.001 HIS B 280 Details of bonding type rmsd covalent geometry : bond 0.00249 (10161) covalent geometry : angle 0.55941 (13780) hydrogen bonds : bond 0.02961 ( 528) hydrogen bonds : angle 4.02289 ( 1536) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: A 60 TYR cc_start: 0.6994 (OUTLIER) cc_final: 0.6575 (m-80) REVERT: B 112 ARG cc_start: 0.6685 (tpt170) cc_final: 0.6040 (tpt-90) REVERT: C 83 MET cc_start: 0.8578 (mtp) cc_final: 0.8347 (mmt) outliers start: 14 outliers final: 7 residues processed: 53 average time/residue: 0.0824 time to fit residues: 6.8194 Evaluate side-chains 45 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 60 TYR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 86 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 9 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 GLN A 444 ASN ** B 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.046885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.039508 restraints weight = 66593.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.040641 restraints weight = 37441.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.041442 restraints weight = 24876.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.041946 restraints weight = 18378.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.042368 restraints weight = 14868.752| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3147 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3147 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.5166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10161 Z= 0.218 Angle : 0.688 7.522 13780 Z= 0.346 Chirality : 0.043 0.134 1572 Planarity : 0.004 0.048 1764 Dihedral : 4.647 21.599 1366 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.90 % Allowed : 9.86 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.25), residues: 1231 helix: 0.29 (0.19), residues: 827 sheet: -0.25 (1.03), residues: 31 loop : -0.56 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 28 TYR 0.016 0.002 TYR B 107 PHE 0.018 0.002 PHE A 538 TRP 0.024 0.002 TRP A 477 HIS 0.009 0.001 HIS B 280 Details of bonding type rmsd covalent geometry : bond 0.00495 (10161) covalent geometry : angle 0.68832 (13780) hydrogen bonds : bond 0.04304 ( 528) hydrogen bonds : angle 4.41336 ( 1536) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 40 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: A 60 TYR cc_start: 0.6989 (OUTLIER) cc_final: 0.6668 (m-80) REVERT: B 328 MET cc_start: 0.8674 (mtt) cc_final: 0.8405 (mtm) REVERT: C 83 MET cc_start: 0.8569 (mtp) cc_final: 0.8318 (mmt) outliers start: 21 outliers final: 10 residues processed: 57 average time/residue: 0.0788 time to fit residues: 7.1729 Evaluate side-chains 44 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 60 TYR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 230 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 101 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 120 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN ** B 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.047967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.040583 restraints weight = 65683.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.041718 restraints weight = 36522.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.042553 restraints weight = 23989.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.043135 restraints weight = 17585.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.043527 restraints weight = 13941.104| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.5255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10161 Z= 0.117 Angle : 0.570 6.417 13780 Z= 0.282 Chirality : 0.040 0.133 1572 Planarity : 0.003 0.036 1764 Dihedral : 4.444 20.357 1366 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.63 % Allowed : 10.68 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.25), residues: 1231 helix: 0.62 (0.19), residues: 816 sheet: -0.03 (1.04), residues: 31 loop : -0.30 (0.34), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 112 TYR 0.019 0.001 TYR B 400 PHE 0.018 0.001 PHE A 538 TRP 0.020 0.001 TRP A 477 HIS 0.002 0.001 HIS B 280 Details of bonding type rmsd covalent geometry : bond 0.00272 (10161) covalent geometry : angle 0.56958 (13780) hydrogen bonds : bond 0.03160 ( 528) hydrogen bonds : angle 4.12356 ( 1536) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 36 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 521 MET cc_start: 0.8008 (mpp) cc_final: 0.7125 (mtm) outliers start: 18 outliers final: 10 residues processed: 50 average time/residue: 0.0786 time to fit residues: 6.3109 Evaluate side-chains 43 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 230 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 42 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.047923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.040627 restraints weight = 65532.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.041798 restraints weight = 36601.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.042608 restraints weight = 24099.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.043162 restraints weight = 17676.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.043557 restraints weight = 14057.319| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3204 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3204 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.5439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 10161 Z= 0.117 Angle : 0.564 7.389 13780 Z= 0.278 Chirality : 0.040 0.131 1572 Planarity : 0.003 0.038 1764 Dihedral : 4.327 19.909 1366 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.45 % Allowed : 11.58 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.25), residues: 1231 helix: 0.77 (0.19), residues: 819 sheet: 0.14 (1.07), residues: 31 loop : -0.29 (0.34), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 221 TYR 0.024 0.001 TYR A 60 PHE 0.017 0.001 PHE A 538 TRP 0.019 0.001 TRP A 477 HIS 0.003 0.001 HIS C 63 Details of bonding type rmsd covalent geometry : bond 0.00276 (10161) covalent geometry : angle 0.56405 (13780) hydrogen bonds : bond 0.03045 ( 528) hydrogen bonds : angle 4.05382 ( 1536) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 33 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 11 residues processed: 47 average time/residue: 0.0662 time to fit residues: 5.2326 Evaluate side-chains 45 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 244 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 0 optimal weight: 10.9990 chunk 18 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 68 optimal weight: 0.4980 chunk 56 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 121 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.047960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.040710 restraints weight = 65044.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.041865 restraints weight = 36225.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.042677 restraints weight = 23864.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.043222 restraints weight = 17496.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.043559 restraints weight = 13909.815| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3207 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3207 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.5622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10161 Z= 0.107 Angle : 0.561 8.915 13780 Z= 0.274 Chirality : 0.040 0.207 1572 Planarity : 0.003 0.038 1764 Dihedral : 4.185 19.941 1366 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.09 % Allowed : 12.04 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.25), residues: 1231 helix: 0.89 (0.19), residues: 819 sheet: 0.23 (1.09), residues: 31 loop : -0.20 (0.34), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 221 TYR 0.012 0.001 TYR B 107 PHE 0.014 0.001 PHE A 538 TRP 0.018 0.001 TRP A 477 HIS 0.002 0.000 HIS C 63 Details of bonding type rmsd covalent geometry : bond 0.00247 (10161) covalent geometry : angle 0.56138 (13780) hydrogen bonds : bond 0.02902 ( 528) hydrogen bonds : angle 3.99663 ( 1536) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 46 average time/residue: 0.0796 time to fit residues: 6.0423 Evaluate side-chains 43 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 230 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 119 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 91 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.047729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.040527 restraints weight = 64928.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.041674 restraints weight = 36114.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.042468 restraints weight = 23785.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.043012 restraints weight = 17488.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.043404 restraints weight = 13937.439| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3201 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3201 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.5773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10161 Z= 0.111 Angle : 0.577 7.943 13780 Z= 0.281 Chirality : 0.040 0.151 1572 Planarity : 0.003 0.039 1764 Dihedral : 4.135 19.612 1366 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.09 % Allowed : 12.13 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.25), residues: 1231 helix: 0.98 (0.19), residues: 813 sheet: 0.02 (1.04), residues: 31 loop : -0.15 (0.34), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 221 TYR 0.024 0.001 TYR B 400 PHE 0.014 0.001 PHE A 538 TRP 0.018 0.001 TRP A 477 HIS 0.002 0.000 HIS C 63 Details of bonding type rmsd covalent geometry : bond 0.00257 (10161) covalent geometry : angle 0.57670 (13780) hydrogen bonds : bond 0.02895 ( 528) hydrogen bonds : angle 3.97740 ( 1536) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 33 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 TYR cc_start: 0.8576 (m-80) cc_final: 0.8201 (m-10) outliers start: 12 outliers final: 11 residues processed: 43 average time/residue: 0.0628 time to fit residues: 4.5808 Evaluate side-chains 44 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 230 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 92 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 61 optimal weight: 0.0970 chunk 59 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.047805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.040619 restraints weight = 64633.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.041772 restraints weight = 36062.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.042494 restraints weight = 23805.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.043094 restraints weight = 17681.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.043500 restraints weight = 14014.737| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3201 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3201 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.5917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10161 Z= 0.107 Angle : 0.569 8.313 13780 Z= 0.276 Chirality : 0.039 0.132 1572 Planarity : 0.003 0.040 1764 Dihedral : 4.059 19.978 1366 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.27 % Allowed : 12.04 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.25), residues: 1231 helix: 1.06 (0.19), residues: 813 sheet: -0.34 (0.98), residues: 31 loop : -0.15 (0.34), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 221 TYR 0.010 0.001 TYR B 107 PHE 0.014 0.001 PHE A 538 TRP 0.018 0.001 TRP A 477 HIS 0.002 0.000 HIS C 63 Details of bonding type rmsd covalent geometry : bond 0.00245 (10161) covalent geometry : angle 0.56855 (13780) hydrogen bonds : bond 0.02804 ( 528) hydrogen bonds : angle 3.94956 ( 1536) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 36 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 TYR cc_start: 0.8591 (m-80) cc_final: 0.8227 (m-10) REVERT: A 521 MET cc_start: 0.8126 (mpp) cc_final: 0.7660 (mtm) outliers start: 14 outliers final: 11 residues processed: 47 average time/residue: 0.0665 time to fit residues: 5.3656 Evaluate side-chains 42 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 31 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 230 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 93 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 95 optimal weight: 0.4980 chunk 57 optimal weight: 0.9980 chunk 116 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 22 optimal weight: 0.0570 chunk 14 optimal weight: 3.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.047734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.040578 restraints weight = 64190.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.041716 restraints weight = 35881.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.042506 restraints weight = 23730.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.043049 restraints weight = 17491.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.043383 restraints weight = 13907.711| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3199 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3199 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.6014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10161 Z= 0.104 Angle : 0.583 11.070 13780 Z= 0.281 Chirality : 0.040 0.356 1572 Planarity : 0.003 0.040 1764 Dihedral : 4.042 20.514 1366 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.00 % Allowed : 12.49 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.25), residues: 1231 helix: 1.07 (0.19), residues: 814 sheet: -0.41 (0.95), residues: 31 loop : -0.10 (0.34), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 221 TYR 0.010 0.001 TYR B 107 PHE 0.014 0.001 PHE A 538 TRP 0.018 0.001 TRP A 477 HIS 0.002 0.000 HIS C 63 Details of bonding type rmsd covalent geometry : bond 0.00239 (10161) covalent geometry : angle 0.58252 (13780) hydrogen bonds : bond 0.02777 ( 528) hydrogen bonds : angle 3.95056 ( 1536) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 TYR cc_start: 0.8547 (m-80) cc_final: 0.8183 (m-10) outliers start: 11 outliers final: 10 residues processed: 42 average time/residue: 0.0702 time to fit residues: 5.0205 Evaluate side-chains 43 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 230 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 63 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 96 optimal weight: 0.0770 chunk 87 optimal weight: 0.9980 chunk 85 optimal weight: 0.0670 chunk 81 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 54 optimal weight: 0.0870 chunk 86 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.3254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 232 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.048325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.041096 restraints weight = 65094.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.042288 restraints weight = 36238.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.043117 restraints weight = 23715.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.043685 restraints weight = 17276.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.044084 restraints weight = 13612.696| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3223 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3223 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.6043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10161 Z= 0.098 Angle : 0.574 10.558 13780 Z= 0.276 Chirality : 0.039 0.314 1572 Planarity : 0.003 0.041 1764 Dihedral : 3.953 20.638 1366 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.81 % Allowed : 12.76 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.25), residues: 1231 helix: 1.11 (0.19), residues: 814 sheet: -0.29 (0.97), residues: 31 loop : -0.15 (0.34), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 498 TYR 0.010 0.001 TYR B 107 PHE 0.013 0.001 PHE A 538 TRP 0.017 0.001 TRP A 477 HIS 0.002 0.000 HIS A 497 Details of bonding type rmsd covalent geometry : bond 0.00214 (10161) covalent geometry : angle 0.57377 (13780) hydrogen bonds : bond 0.02536 ( 528) hydrogen bonds : angle 3.90589 ( 1536) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1442.58 seconds wall clock time: 25 minutes 43.45 seconds (1543.45 seconds total)